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Class: EntityToDiseaseOrPhenotypicFeatureAssociationMixin

Description: A mixin applied to any association whose object (target node) is a disease or a phenotypic feature. Provides the shared qualifier vocabulary for such statements; subtypes narrow the object range to a disease or to a phenotypic feature specifically.
classDiagram class EntityToDiseaseOrPhenotypicFeatureAssociationMixin FrequencyQualifierMixin <|-- EntityToDiseaseOrPhenotypicFeatureAssociationMixin EntityToDiseaseOrPhenotypicFeatureAssociationMixin <|-- CellLineToDiseaseOrPhenotypicFeatureAssociation EntityToDiseaseOrPhenotypicFeatureAssociationMixin <|-- ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation EntityToDiseaseOrPhenotypicFeatureAssociationMixin <|-- ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation EntityToDiseaseOrPhenotypicFeatureAssociationMixin <|-- ChemicalOrDrugOrTreatmentAdverseEventAssociation EntityToDiseaseOrPhenotypicFeatureAssociationMixin <|-- ChemicalOrDrugOrTreatmentSideEffectAssociation EntityToDiseaseOrPhenotypicFeatureAssociationMixin <|-- MaterialSampleToDiseaseOrPhenotypicFeatureAssociation EntityToDiseaseOrPhenotypicFeatureAssociationMixin <|-- EntityToPhenotypicFeatureAssociationMixin EntityToDiseaseOrPhenotypicFeatureAssociationMixin <|-- EntityToDiseaseAssociationMixin EntityToDiseaseOrPhenotypicFeatureAssociationMixin : anatomical_context_qualifier EntityToDiseaseOrPhenotypicFeatureAssociationMixin : disease_context_qualifier EntityToDiseaseOrPhenotypicFeatureAssociationMixin --|> Disease : disease_context_qualifier EntityToDiseaseOrPhenotypicFeatureAssociationMixin : frequency_qualifier EntityToDiseaseOrPhenotypicFeatureAssociationMixin : object EntityToDiseaseOrPhenotypicFeatureAssociationMixin --|> DiseaseOrPhenotypicFeature : object EntityToDiseaseOrPhenotypicFeatureAssociationMixin : object_aspect_qualifier EntityToDiseaseOrPhenotypicFeatureAssociationMixin --|> GeneOrGeneProductOrChemicalEntityAspectEnum : object_aspect_qualifier EntityToDiseaseOrPhenotypicFeatureAssociationMixin : object_direction_qualifier EntityToDiseaseOrPhenotypicFeatureAssociationMixin --|> DirectionQualifierEnum : object_direction_qualifier EntityToDiseaseOrPhenotypicFeatureAssociationMixin : object_specialization_qualifier EntityToDiseaseOrPhenotypicFeatureAssociationMixin : population_context_qualifier EntityToDiseaseOrPhenotypicFeatureAssociationMixin --|> PopulationOfIndividualOrganisms : population_context_qualifier EntityToDiseaseOrPhenotypicFeatureAssociationMixin : predicate EntityToDiseaseOrPhenotypicFeatureAssociationMixin : qualified_predicate EntityToDiseaseOrPhenotypicFeatureAssociationMixin : subject EntityToDiseaseOrPhenotypicFeatureAssociationMixin --|> NamedThing : subject EntityToDiseaseOrPhenotypicFeatureAssociationMixin : subject_aspect_qualifier EntityToDiseaseOrPhenotypicFeatureAssociationMixin --|> GeneOrGeneProductOrChemicalEntityAspectEnum : subject_aspect_qualifier EntityToDiseaseOrPhenotypicFeatureAssociationMixin : subject_direction_qualifier EntityToDiseaseOrPhenotypicFeatureAssociationMixin --|> DirectionQualifierEnum : subject_direction_qualifier EntityToDiseaseOrPhenotypicFeatureAssociationMixin : subject_specialization_qualifier

Inheritance

Slots

Name Cardinality and Range Inheritance Examples
subject_aspect_qualifier:
Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement). 		0..1
GeneOrGeneProductOrChemicalEntityAspectEnum		 direct stability, abundance, expression, exposure
subject_direction_qualifier:
Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement). 		0..1
DirectionQualifierEnum		 direct increased, downregulated
object_aspect_qualifier:
Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement). 		0..1
GeneOrGeneProductOrChemicalEntityAspectEnum		 direct stability, abundance, expression, exposure
object_direction_qualifier:
Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement). 		0..1
DirectionQualifierEnum		 direct increased, downregulated
qualified_predicate:
Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading. 		0..1
Uriorcurie		 direct biolink:causes
disease_context_qualifier:
A context qualifier representing a disease or condition in which a relationship expressed in an association took place. 		0..1
Disease		 direct MONDO:0004979, MONDO:0005148
subject_specialization_qualifier:
A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier. 		0..1
Uriorcurie		 direct
object_specialization_qualifier:
A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier. 		0..1
Uriorcurie		 direct
anatomical_context_qualifier:
A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location). 		*
String		 direct UBERON:0000178, UBERON:0000956, GO:0005794
population_context_qualifier:
a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association. 		0..1
PopulationOfIndividualOrganisms		 direct
frequency_qualifier:
a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject 		0..1
FrequencyValue		 FrequencyQualifierMixin
subject:
connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object. 		1
NamedThing		 FrequencyQualifierMixin
predicate:
Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats 		1
Uriorcurie		 FrequencyQualifierMixin
object:
disease or phenotype 		1
DiseaseOrPhenotypicFeature		 FrequencyQualifierMixin MONDO:0017314, MP:0013229

Mixin Usage

mixed into description
CellLineToDiseaseOrPhenotypicFeatureAssociation An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype.
ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype.
ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the chemical or treatment is used to treat, or is being studied to treat, the disease or phenotypic feature.
ChemicalOrDrugOrTreatmentAdverseEventAssociation This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disease or phenotypic feature is an untoward medical occurrence that happens during treatment, whether or not considered related to the treatment.
ChemicalOrDrugOrTreatmentSideEffectAssociation This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disease or phenotypic feature is an unintended, but predictable, secondary effect of the treatment.
MaterialSampleToDiseaseOrPhenotypicFeatureAssociation An association between a material sample and a disease or phenotype.

LinkML Source

name: entity to disease or phenotypic feature association mixin
description: A mixin applied to any association whose object (target node) is a disease
  or a phenotypic feature. Provides the shared qualifier vocabulary for such statements;
  subtypes narrow the object range to a disease or to a phenotypic feature specifically.
from_schema: https://w3id.org/biolink/vocab/
is_a: frequency qualifier mixin
mixin: true
slots:
- subject aspect qualifier
- subject direction qualifier
- object aspect qualifier
- object direction qualifier
- qualified predicate
- disease context qualifier
- subject specialization qualifier
- object specialization qualifier
- anatomical context qualifier
- population context qualifier
slot_usage:
  object:
    name: object
    description: disease or phenotype
    examples:
    - value: MONDO:0017314
      description: Ehlers-Danlos syndrome, vascular type
    - value: MP:0013229
      description: abnormal brain ventricle size
    range: disease or phenotypic feature
defining_slots:
- subject
- predicate
- object